SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production

The UK Synthetic Biology Research Centre, SYNBIOCHEM, hosted by the Manchester Institute of Biotechnology at the University of Manchester is delivering innovative technology platforms to facilitate the predictable engineering of microbial bio-factories for fine and speciality chemicals production. We provide an overview of our foundry activities that are being applied to grand challenge projects to deliver innovation in bio-based chemicals production for industrial biotechnology.

[1]  C. Weizmann,et al.  The activation of the butanol-acetone fermentation of carbohydrates by Clostridium acetobutylicum (Weizmann). , 1937, The Biochemical journal.

[2]  Andrew Currin,et al.  SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution , 2014, Protein engineering, design & selection : PEDS.

[3]  Rainer Breitling,et al.  Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle , 2016, Natural product reports.

[4]  E. Hayden Synthetic-biology firms shift focus , 2014, Nature.

[5]  Mark D. White,et al.  UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis , 2015, Nature.

[6]  Christopher A. Voigt,et al.  Synthetic biology to access and expand nature's chemical diversity , 2016, Nature Reviews Microbiology.

[7]  Kai Blin,et al.  antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..

[8]  Neil Swainston,et al.  An analysis of a ‘community-driven’ reconstruction of the human metabolic network , 2013, Metabolomics.

[9]  N. Scrutton,et al.  Conversion of alcohols to enantiopure amines through dual-enzyme hydrogen-borrowing cascades , 2015, Science.

[10]  Tim Cushnie,et al.  Alkaloids: an overview of their antibacterial, antibiotic-enhancing and antivirulence activities. , 2014, International journal of antimicrobial agents.

[11]  Matthew R. Pocock,et al.  SBOL Visual: A Graphical Language for Genetic Designs , 2015, PLoS biology.

[12]  Mark S Dunstan,et al.  Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species. , 2014, Journal of the American Chemical Society.

[13]  F. Parmeggiani,et al.  Rapid and sensitive monitoring of biocatalytic reactions using ion mobility mass spectrometry. , 2016, The Analyst.

[14]  E. Takano,et al.  A ‘Plug and Play’ Platform for the Production of Diverse Monoterpene Hydrocarbon Scaffolds in Escherichia coli , 2016, ChemistrySelect.

[15]  Division on Earth Industrialization of Biology , 2015 .

[16]  M. Friedman Overview of antibacterial, antitoxin, antiviral, and antifungal activities of tea flavonoids and teas , 2006, Molecular nutrition & food research.

[17]  Neil Swainston,et al.  Recon 2.2: from reconstruction to model of human metabolism , 2016, Metabolomics.

[18]  Pablo Carbonell,et al.  SensiPath: computer-aided design of sensing-enabling metabolic pathways , 2016, Nucleic Acids Res..

[19]  Pablo Carbonell,et al.  Semisupervised Gaussian Process for Automated Enzyme Search. , 2016, ACS synthetic biology.

[20]  Zhen Zhang,et al.  Sharing Structure and Function in Biological Design with SBOL 2.0. , 2016, ACS synthetic biology.

[21]  D. Kell,et al.  Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. , 2015, Trends in biotechnology.

[22]  Carole Goble,et al.  SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals , 2016, Biochemical Society transactions.

[23]  William F. Furter,et al.  A Century of chemical engineering , 1982 .

[24]  Neil Swainston,et al.  RobOKoD: microbial strain design for (over)production of target compounds , 2015, Front. Cell Dev. Biol..

[25]  Kang Lan Tee,et al.  Single-step fermentative production of the cholesterol-lowering drug pravastatin via reprogramming of Penicillium chrysogenum , 2015, Proceedings of the National Academy of Sciences.

[26]  Christoph Steinbeck,et al.  ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..

[27]  Susanna Zucca,et al.  Advances and Computational Tools towards Predictable Design in Biological Engineering , 2014, Comput. Math. Methods Medicine.

[28]  Jason Micklefield,et al.  Rational Re-engineering of a Transcriptional Silencing PreQ1 Riboswitch. , 2015, Journal of the American Chemical Society.

[29]  Christoph Steinbeck,et al.  libChEBI: an API for accessing the ChEBI database , 2016, Journal of Cheminformatics.

[30]  Neil Swainston,et al.  GeneGenie: optimized oligomer design for directed evolution , 2014, Nucleic Acids Res..

[31]  C. Smolke,et al.  Complete biosynthesis of opioids in yeast , 2015, Science.

[32]  Kate Bulpin,et al.  Synthetic Biology , 2016, Palgrave Macmillan UK.

[33]  J. Keasling,et al.  Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development , 2014, Nature Reviews Microbiology.

[34]  G. Pastore,et al.  Bio-oxidation of terpenes: an approach for the flavor industry. , 2009, Chemical reviews.

[35]  Rainer Breitling,et al.  Judging synthetic biology risks , 2015, Science.

[36]  Pablo Carbonell,et al.  Retropath: automated pipeline for embedded metabolic circuits. , 2014, ACS synthetic biology.

[37]  R. Goodacre,et al.  Metabolomic analysis of riboswitch containing E. coli recombinant expression system. , 2016, Molecular bioSystems.

[38]  Eriko Takano,et al.  Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli. , 2015, ACS synthetic biology.

[39]  R. Goodacre,et al.  Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block. , 2015, ACS synthetic biology.

[40]  Andrew Currin,et al.  Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently , 2014, Chemical Society reviews.

[41]  R. Breitling,et al.  PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis. , 2011, Analytical chemistry.

[42]  Patrik R. Jones,et al.  A microbial platform for renewable propane synthesis based on a fermentative butanol pathway , 2015, Biotechnology for Biofuels.

[43]  H. Alper,et al.  Synthetic Biology for Specialty Chemicals. , 2015, Annual review of chemical and biomolecular engineering.

[44]  Rebecca Beveridge,et al.  New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition , 2015, Nature.